I ran a custom loop the other day to get some twitter information. Since I was running the code in a template and that template was being called from another loop, I was able to get the template data by doing this

$content = $template->post_content;
echo $content;

I figured this would be better than setting up another loop. When I did this, I found that the content was unformatted. So doing a little research, I found that if I pass it through the content filter

So naturally, I figured that if I pass $query through the same content filter that it would fix my issue. Nope, I was wrong. Is there a way to get the function to filter the return $query through the_content filter?